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Source code for galaxy.util.checkers

import gzip
import re
import sys
import zipfile

from six import StringIO

from galaxy import util
from galaxy.util.image_util import image_type

if sys.version_info < (3, 3):
    import bz2file as bz2
else:
    import bz2

HTML_CHECK_LINES = 100


[docs]def check_html(file_path, chunk=None): if chunk is None: temp = open(file_path, "U") elif hasattr(chunk, "splitlines"): temp = chunk.splitlines() else: temp = chunk regexp1 = re.compile("<A\s+[^>]*HREF[^>]+>", re.I) regexp2 = re.compile("<IFRAME[^>]*>", re.I) regexp3 = re.compile("<FRAMESET[^>]*>", re.I) regexp4 = re.compile("<META[\W][^>]*>", re.I) regexp5 = re.compile("<SCRIPT[^>]*>", re.I) lineno = 0 # TODO: Potentially reading huge lines into string here, this should be # reworked. for line in temp: lineno += 1 matches = regexp1.search(line) or regexp2.search(line) or regexp3.search(line) or regexp4.search(line) or regexp5.search(line) if matches: if chunk is None: temp.close() return True if HTML_CHECK_LINES and (lineno > HTML_CHECK_LINES): break if chunk is None: temp.close() return False
[docs]def check_binary(name, file_path=True): # Handles files if file_path is True or text if file_path is False is_binary = False if file_path: temp = open(name, "U") else: temp = StringIO(name) try: for char in temp.read(100): if util.is_binary(char): is_binary = True break finally: temp.close() return is_binary
[docs]def check_gzip(file_path, check_content=True): # This method returns a tuple of booleans representing ( is_gzipped, is_valid ) # Make sure we have a gzipped file try: temp = open(file_path, "U") magic_check = temp.read(2) temp.close() if magic_check != util.gzip_magic: return (False, False) except: return (False, False) # We support some binary data types, so check if the compressed binary file is valid # If the file is Bam, it should already have been detected as such, so we'll just check # for sff format. try: header = gzip.open(file_path).read(4) if header == b'.sff': return (True, True) except: return(False, False) if not check_content: return (True, True) CHUNK_SIZE = 2 ** 15 # 32Kb gzipped_file = gzip.GzipFile(file_path, mode='rb') chunk = gzipped_file.read(CHUNK_SIZE) gzipped_file.close() # See if we have a compressed HTML file if check_html(file_path, chunk=chunk): return (True, False) return (True, True)
[docs]def check_bz2(file_path, check_content=True): try: temp = open(file_path, "U") magic_check = temp.read(3) temp.close() if magic_check != util.bz2_magic: return (False, False) except: return(False, False) if not check_content: return (True, True) CHUNK_SIZE = 2 ** 15 # reKb bzipped_file = bz2.BZ2File(file_path, mode='rb') chunk = bzipped_file.read(CHUNK_SIZE) bzipped_file.close() # See if we have a compressed HTML file if check_html(file_path, chunk=chunk): return (True, False) return (True, True)
[docs]def check_zip(file_path): if zipfile.is_zipfile(file_path): return True return False
[docs]def is_bz2(file_path): is_bz2, is_valid = check_bz2(file_path, check_content=False) return is_bz2
[docs]def is_gzip(file_path): is_gzipped, is_valid = check_gzip(file_path, check_content=False) return is_gzipped
[docs]def check_image(file_path): """ Simple wrapper around image_type to yield a True/False verdict """ if image_type(file_path): return True return False
__all__ = ( 'check_binary', 'check_bz2', 'check_gzip', 'check_html', 'check_image', 'check_zip', 'is_gzip', 'is_bz2', )